RetrogeneDB ID:

retro_pabe_1289

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:15:39249751..39251090(-)
Located in intron of:ENSPPYG00000006404
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DKFZP468F2127
Ensembl ID:ENSPPYG00000004562
Aliases:None
Description:keratin, type II cytoskeletal 8 [Source:RefSeq peptide;Acc:NP_001127365]


Retrocopy-Parental alignment summary:






>retro_pabe_1289
TCCTCGAGCTTCTCCCGAATGGGCAGCAGCAGCTTCTGGGGTGGCCTGGGTGCAGGATATGGTGGGGCCAGTGGAGGCAT
CACCGCCGTCACTGTCAACCAAAGCCTGCTGAGCCCTCTTAACCTGGAGGTGGACCCCAACATCCAGGCTGTGCGCACCC
AGGAGGAGAAGCAGATCAAGACCCTCAACAACAAGTTTGCCTCTTTCATAGACAAGGTACGGTTCCTGGAGCAGCAGAAC
AAGATGCTGGAGACCAAGTGGAGCCTTGTGCAGCAGCAGAAGATGGCTTGGAGCAACATGGACAACATGTTCGAGAGCTA
CATCAACAACATTAGGTGGCAGCTGGAGACTCTGGGTCAGGAGAAGCTGAAGCTGGAGGCGGAGCTTGGCAGCATGCACG
GGCTGGTGGAAGACTTCAGGAACAAGTATGAGGATGAGATCAGTAAGCGTACAGAGATGGAGAATGAATTTGTGCTCATC
AAGGAGGATGTGGATGAAGCTTATGTGAACAAGATGGAGCTGGAGTCTCCCCTGAAAGGGCTGACTGCCAAGATCAGCTT
CCTCAGGTAGCTGTGTGAAGAGGAGATCGGGAGCTGCAGTCCCAGATCTCGGATACATCTGTGGTGCTGTTCATGGACAA
TAGCCGCTTCCTGGACATGGACAGTATCATCCCTGAGGTCAAGGTGCAGTACGAGGAGATTGCCAACCGCAGCCGGGCTG
AGGCTGAGAGCATGTACTAGATCAAGTATAAGGAACTGCAGACGCTGGATCGGAAGCGTGGGGATGACCTGTGGCGTGCA
AAGACTGAGATCTCCTAGATGAACCGGAACATCAGCCAGCTCCAAGCTGAGACTGAGGGTCTCAAAGGCCAGAGGGCTTC
CCCGGAGGCCGCCACGCAGATACCGAGCAGCATGCGGAGCTAGCCATTAAGGATGCCAACGCCAAGCTGTCTGAGCTGGA
GGCCACCCTGCAGCTAGCCAGTCAAGACATGGCATGGCAGCTGCGTGAGTACCAGGAGCTGATGAATGTCAAGCTGGCCC
TGGATATCAAGATTGCCACCTACAGGAAGCTGTTGGAGGGTGAGGAGAGCTGGCTGGAGTCTGGGATGCAGAACATGAGT
ATCCATATGAAGACCACCAGCAGCTATGCAGGTGGTCAGAGCTTGGCCTATGGGGGCCTCACAAGCCCTGGTGTCAGCTA
CGGCCTGGGCTCCAGCTTTGGCTTTGGCATGGGCTCCAGCTCCTTCAGCTGCACCAGCTCCTTCAGGGCCGTGGTCGTGA
AGAAGATCGAAACCTGTGATGGGAAGCTGGTGTCTGAGTCCTCCGATGTCCTGCCCAAG

ORF - retro_pabe_1289 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.63 %
Parental protein coverage: 99.55 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSSSSSRVSSSFGLGGYG---GSGMGGITAVTVNQSL-SPV-LEVDPNI-AVRTQEKEQIKTLNNKFASFI
SSS.SR..SS...GG.G...G...GGITAVTVNQSL.SP..LEVDPNI.AVRTQE..QIKTLNNKFASFI
RetrocopySSSFSRMGSSSFWGGLGAGYGGASGGITAVTVNQSLLSPLNLEVDPNIQAVRTQEEKQIKTLNNKFASFI
ParentalDKVRFLEQQNKMLETKWSLLQQQKTARSNMDNMFESYINNLRRQLETLGQEKLKLEAELGNMQGLVEDFK
DKVRFLEQQNKMLETKWSL.QQQK.A.SNMDNMFESYINN.R.QLETLGQEKLKLEAELG.M.GLVEDF.
RetrocopyDKVRFLEQQNKMLETKWSLVQQQKMAWSNMDNMFESYINNIRWQLETLGQEKLKLEAELGSMHGLVEDFR
ParentalNKYEDEINKRTEMENEFVLIKKDVDEAYMNKVELESRLEGLTDEINFLRQLYEEEI-RELQSQISDTSVV
NKYEDEI.KRTEMENEFVLIK.DVDEAY.NK.ELES.L.GLT..I.FLR.L.EEEI.RELQSQISDTSVV
RetrocopyNKYEDEISKRTEMENEFVLIKEDVDEAYVNKMELESPLKGLTAKISFLR*LCEEEI<RELQSQISDTSVV
ParentalLSMDNSRSLDMDSIIAEVKAQYEDIANRSRAEAESMYQIKYEELQSLAGKHGDDLRRTKTEISEMNRNIS
L.MDNSR.LDMDSII.EVK.QYE.IANRSRAEAESMY.IKY.ELQ.L..K.GDDL.R.KTEIS.MNRNIS
RetrocopyLFMDNSRFLDMDSIIPEVKVQYEEIANRSRAEAESMY*IKYKELQTLDRKRGDDLWRAKTEIS*MNRNIS
ParentalRLQAEIEGLKGQRASLEAAI-ADAEQRGELAIKDANAKLSELEAALQRAKQDMARQLREYQELMNVKLAL
.LQAE.EGLKGQRAS.EAA..AD.EQ..ELAIKDANAKLSELEA.LQ.A.QDMA.QLREYQELMNVKLAL
RetrocopyQLQAETEGLKGQRASPEAAT<ADTEQHAELAIKDANAKLSELEATLQLASQDMAWQLREYQELMNVKLAL
ParentalDIEIATYRKLLEGEESRLESGMQNMSIHTKTTSGYAGGLSSAYGGLTSPGLSYGLGSSFGSGAGSSSFSR
DI.IATYRKLLEGEES.LESGMQNMSIH.KTTS.YAGG.S.AYGGLTSPG.SYGLGSSFG.G.GSSSFS.
RetrocopyDIKIATYRKLLEGEESWLESGMQNMSIHMKTTSSYAGGQSLAYGGLTSPGVSYGLGSSFGFGMGSSSFSC
ParentalTSSSRAVVVKKIETRDGKLVSESSDLLPK
TSS.RAVVVKKIET.DGKLVSESSD.LPK
RetrocopyTSSFRAVVVKKIETCDGKLVSESSDVLPK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 0 .06 RPM 0 .55 RPM
SRP007412_cerebellum 0 .61 RPM 0 .12 RPM
SRP007412_heart 0 .06 RPM 23 .57 RPM
SRP007412_kidney 0 .13 RPM 106 .83 RPM
SRP007412_liver 0 .12 RPM 163 .17 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1289 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1289 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1289 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1557

Parental genes homology:
Parental genes homology involve 17 parental genes, and 152 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000071992 retrocopies
Callithrix jacchus ENSCJAG000000181473 retrocopies
Cavia porcellus ENSCPOG000000026155 retrocopies
Dasypus novemcinctus ENSDNOG000000074003 retrocopies
Felis catus ENSFCAG000000002982 retrocopies
Homo sapiens ENSG0000017042128 retrocopies
Gorilla gorilla ENSGGOG0000001467318 retrocopies
Macaca mulatta ENSMMUG0000000216322 retrocopies
Mustela putorius furoENSMPUG000000064417 retrocopies
Mus musculus ENSMUSG000000493821 retrocopy
Nomascus leucogenys ENSNLEG000000177338 retrocopies
Oryctolagus cuniculus ENSOCUG000000069451 retrocopy
Otolemur garnettii ENSOGAG0000001174016 retrocopies
Pongo abelii ENSPPYG000000045481 retrocopy
Pongo abelii ENSPPYG00000004562 31 retrocopies
Pteropus vampyrus ENSPVAG000000093603 retrocopies
Rattus norvegicus ENSRNOG000000097791 retrocopy



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